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Table 2 Examples of bioinformatic software utilizing sketching algorithms

From: When the levee breaks: a practical guide to sketching algorithms for processing the flood of genomic data

Software Purpose Sketching algorithm
GROOT [25] Variant detection in metagenomes MinHash (KHF)
mashtree [26] Phylogenetic tree construction MinHash (KMV)
MashMap [27] Long read alignment Minimizer/MinHash (KMV)
MASH [1] Sequence analysis MinHash (KMV)
sourmash [22] Sequence analysis MinHash (KMV)
finch [23] Sequence analysis MinHash (KMV)
MiniMap2 [28] Read alignment Minimizer
ABySS [29] Genome assembly Bloom filter
Lighter [30] Sequencing error correction Bloom filter
BIGSI [31] Sequence index and search Bloom filter
khmer [32] Sequence analysis Count-Min sketch
FastEtch [33] Genome assembly Count-Min sketch
dashing [2] Sequence analysis HyperLogLog
krakenUniq [34] Metagenome classification HyperLogLog
HULK [4] Sequence analysis Histosketch
ntCard [35] Sequence analysis ntCard
BBsketch [24] Sequence analysis MinHash
MHAP [21] Genome assembly MinHash
MC-MinH [20] Sequence clustering MinHash
KmerGenie [36] Sequence analysis Count-Min sketch variant
Squeakr [37] Sequence analysis Counting Quotient Filter
Mantis [38] Sequence index and search Counting Quotient Filter
kssd [39] Sequence analysis K-mer Substring Space Decomposition
  1. An up-to-date list is provided in [40]